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Background The Abies koreana (Korean fir) population is declining at an accelerating rate on Mt. Hallasan in Jeju Island, Republic of Korea. Several prior studies have reported various inconclusive reasons, indicating that additional data, such as data on microbial communities that promote plant growth and resistance to abiotic stresses, are required to further understand the phenomena. To the best of our knowledge, this is the first investigation that documents the changes in the microbial community as the result of the decline of the Korean fir forest. Here, high throughput sequencing data were provided for the rhizosphere microbiome of a Korean fir, identifying the bacterial and fungal composition differences between the rhizosphere soil of healthy Korean fir (HKF) and dead Korean fir (DKF). Results The results showed that the DKF soil of the fungal community was distinctly separated from the HKF soil. Interestingly, HKF soil comprised dominant symbiotic fungi (Russula, Sebacina, Inocybe, and Phenoliferia), whereas the microbial composition in DKF samples comprised abundant saprotrophs, such as Trichoderma, Ascocoryne, and Umbelopsis. It was also observed that symbiotic fungi, such as Russula, act as a hub in the co-occurrence network. Additionally, the representative fungal genera in HKF soil had a strong positive correlation with only a few soil physicochemical features: K+, Na+, Avail P, and cation exchange capacity (CEC). Conclusions Our findings shed light on the rhizosphere microbiota of dead and live A. koreana plants and their relationship with edaphic factors. The woody plant-associated symbiotic fungi, including ECMs, was also highlighted as a potential strategy to enhance the Korean fir forest ecosystem health.